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BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains Review

Journal Journal of Biomedical Semantics
ISSN: 2041-1480
Output data Year: 2014, Volume: 5, Number: 1, Article number : 5, Pages count : DOI: 10.1186/2041-1480-5-5
Authors Katayama Toshiaki 1 , Wilkinson Mark D. 2 , Aoki-Kinoshita Kiyoko F. 3 , Kawashima Shuichi 1 , Yamamoto Yasunori 1 , Yamaguchi Atsuko 1 , Okamoto Shinobu 1 , Kawano Shin 1 , Kim Jin Dong 1 , Wang Yue 1 , Wu Hongyan 1 , Kano Yoshinobu 4 , Ono Hiromasa 1 , Bono Hidemasa 1 , Kocbek Simon 1 , Aerts Jan 5,6 , Akune Yukie 3 , Antezana Erick 7 , Arakawa Kazuharu 8 , Aranda Bruno 9 , Baran Joachim 10 , Bolleman Jerven 11 , Bonnal Raoul J.P. 12 , Buttigieg Pier Luigi 13 , Campbell Matthew P. 14 , Chen Yi An 15 , Chiba Hirokazu 16 , Cock Peter J.A. 17 , Cohen K.Bretonnel 18 , Constantin Alexandru 19 , Duck Geraint 19 , Dumontier Michel 20 , Fujisawa Takatomo 21 , Fujiwara Toyofumi 22 , Goto Naohisa 23 , Hoehndorf Robert 24 , Igarashi Yoshinobu 15 , Itaya Hidetoshi 8 , Ito Maori 15 , Iwasaki Wataru 25 , Kalaš Matúš 26 , Katoda Takeo 3 , Kim Taehong 27 , Kokubu Anna 3 , Komiyama Yusuke 28 , Kotera Masaaki 29 , Laibe Camille 30 , Lapp Hilmar 31 , Lütteke Thomas 32 , Marshall M.Scott 33 , Mori Takaaki 3 , Mori Hiroshi 34 , Morita Mizuki 35 , Murakami Katsuhiko 36 , Nakao Mitsuteru 37 , Narimatsu Hisashi 38 , Nishide Hiroyo 16 , Nishimura Yosuke 29 , Nystrom-Persson Johan 15 , Ogishima Soichi 39 , Okamura Yasunobu 40 , Okuda Shujiro 41 , Oshita Kazuki 8 , Packer Nicki H. 42 , Prins Pjotr 43 , Ranzinger Rene 44 , Rocca-Serra Philippe 45 , Sansone Susanna 45 , Sawaki Hiromichi 38 , Shin Sung Ho 27 , Splendiani Andrea 46,47 , Strozzi Francesco 48 , Tadaka Shu 40 , Toukach Philip 49 , Uchiyama Ikuo 16 , Umezaki Masahito 50 , Vos Rutger 51 , Whetzel Patricia L. 52 , Yamada Issaku 53 , Yamasaki Chisato 36,15 , Yamashita Riu 54 , York William S. 44 , Zmasek Christian M. 55 , Kawamoto Shoko 1 , Takagi Toshihisa 56
Affiliations
1 Database Center for Life Science, Research Organization of Information and Systems, 2-11-16, Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan
2 Centro de Biotecnología y Genómica de Plantas UPM-INIA (CBGP), Universidad Politécnica de Madrid, Campus Montegancedo, 28223-Pozuelo de, Alarcón, Spain
3 Department of Bioinformatics, Faculty of Engineering, Soka University, 1-236 Tangi-machi, Hachioji, Tokyo, 192-8577, Japan
4 National Institute of Informatics, JST PRESTO, 2-1-2 Hitotsubashi, Chiyoda-ku, Tokyo, 101-8430, Japan
5 Department of Electrical Engineering (ESAT/SCD), University of Leuven, Kasteelpark Arenberg 10, Leuven, 3001, Belgium
6 iMinds Future Health Department, University of Leuven, Kasteelpark Arenberg 10, Leuven 3001, Belgium
7 Department of Biology, Norwegian University of Science and Technology (NTNU), Høgskoleringen 5, Trondheim, N-7491, Norway
8 Institute for Advanced Biosciences, Keio University, Endo 5322, Fujisawa, Kanagawa, 252-0882, Japan
9 Silicon Cat Ltd, 5 York Road, London, HA6 1JJ, UK
10 Ontario Institute for Cancer Research, 101 College Street, Suite 800, Toronto, Ontario, M5G 0A3, Canada
11 SIB Swiss Institute of Bioinformatics, CMU, rue Michel Servet, Geneve, 4 1211, Switzerland
12 Integrative Biology Program, Istituto Nazionale Genetica Molecolare, Milan, 20122, Italy
13 The Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, Bremerhaven, 27570, Germany
14 Biomolecular Frontiers Research Centre, Macquarie University, North Ryde, NSW, 2109, Australia
15 National Institute of Biomedical Innovation, 7-6-8 Asagi Saito, Ibaraki-City, Osaka, 567-0085, Japan
16 National Institute for Basic Biology, National Institutes of Natural Sciences, Nishigonaka 38, Myodaiji, Okazaki, Aichi, 444-8585, Japan
17 The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
18 Center for Computational Pharmacology, University of Colorado Denver School of Medicine, Aurora, CO, 80045, USA
19 School of Computer Science, The University of Manchester, Oxford Road, M13 9PL, UK
20 Department of Biology, Institute of Biochemistry, School of Computer Science, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, K1S 5B6, Canada
21 Center for Information Biology, National Institute of Genetics, Research Organization of Information and Systems, 1111 Yata, Mishima, Shizuoka, 411-08540, Japan
22 INTEC Inc, 1-3-3 Shinsuna, Koto-ku, Tokyo, 136-8637, Japan
23 Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
24 Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3EG, UK
25 Atmosphere and Ocean Research Institute, the University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8564, Japan
26 Computational Biology Unit, Uni Computing and Department of Informatics, University of Bergen, Thormøhlensgate 55, Bergen, 5008, Norway
27 Korea Institute of Science Technology and Information, 245 Daehangno, Yuseong, Daejeon, 305-806, Korea
28 Department of Biotechnology, Bioinformation Engineering Laboratory, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
29 Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
30 EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
31 National Evolutionary Synthesis Center (NESCent), 2024 W. Main St, Durham, NC, USA
32 Justus-Liebig-University Giesse, Institute of Veterinary Physiology and Biochemistry, Frankfurter Str. 100, Giessen, 35392, Germany
33 MAASTRO Clinic, Maastricht, Postbus 3035, Maastricht, 6202 NA, The Netherlands
34 Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 B-36, Nagatsuta-cho, Midori-ku, Yokohama, 226-8501, Japan
35 Center for Knowledge Structuring, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan
36 Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, Aomi 2-4-7, Koto-ku, Tokyo, 135-0064, Japan
37 Next Generation Systems Core Function Unit, Eisai Product Creation Systems, Eisai Co., Ltd, 5-3-1 Toukoudai, Tsukuba, Ibaraki, 300-2635, Japan
38 Research Center for Medical Glycoscience, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki, 305-8568, Japan
39 Department of Bioclinical informatics, Tohoku Medical Megabank Organization, Tohoku University, Seiryo-cho 4-1, Aoba-ku, Sendai-shi, Miyagi, 980-8575, Japan
40 Graduate School of Information Sciences (GSIS), Tohoku University, 6-3-09 Aoba, Aramaki-aza, Aoba-ku, Sendai, Miyagi, 980-8575, Japan
41 Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata, 951-8510, Japan
42 Biomolecular Frontiers Research Centre, Macquarie University, North Ryde, NSW 2109, Australia
43 Laboratory of Nematology, Droevendaalsesteeg 1, Wageningen University, Wageningen, Netherlands
44 Department of Biochemistry and Molecular Biology, The University of Georgia, 315 Riverbend Road, Athens, GA, 30602, USA
45 Oxford e-Research Center, University of Oxford, Oxford, OX1 3QG, UK
46 Digital Enterprise Research Institute, IDA Business Park, Lower Dangan, Galway, Ireland
47 intelliLeaf.com, Cambridge, UK
48 CeRSA, Parco Tecnologico Padano, Lodi, 26900, Italy
49 Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky prospekt 47, Moscow, 119991, Russia
50 Division of International Cooperative Research, Research Center for Ethnomedicine, Institute of Natural Medicine, University of Toyama, 2630 Sugitani, Toyama, 930-0194, Japan
51 Naturalis Biodiversity Center, Postbus 9517, Leiden, 2300 RA, the Netherlands
52 Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA, 94305-5479, USA
53 Laboratory of Glyco-organic Chemistry, The Noguchi Institute, 1-8-1 Kaga, Itabashi-ku, Tokyo, 173-0003, Japan
54 Tohoku Medical Megabank Organization, Tohoku University, Research Building No.3, 6-3-09 Aoba, Aramaki-aza, Aoba-ku, Sendai, Miyagi, 980-8575, Japan
55 Program on Bioinformatics and Systems Biology, Sanford-Burnham Medical Research Institute, La Jolla, CA, 92037, USA
56 Department of Computational Biology, University of Tokyo, Kashiwa, Chiba, 277-8568, Japan

Abstract: The application of semantic technologies to the integration of biological data and the interoperability of bioinformatics analysis and visualization tools has been the common theme of a series of annual BioHackathons hosted in Japan for the past five years. Here we provide a review of the activities and outcomes from the BioHackathons held in 2011 in Kyoto and 2012 in Toyama. In order to efficiently implement semantic technologies in the life sciences, participants formed various sub-groups and worked on the following topics: Resource Description Framework (RDF) models for specific domains, text mining of the literature, ontology development, essential metadata for biological databases, platforms to enable efficient Semantic Web technology development and interoperability, and the development of applications for Semantic Web data. In this review, we briefly introduce the themes covered by these sub-groups. The observations made, conclusions drawn, and software development projects that emerged from these activities are discussed.
Cite: Katayama T. , Wilkinson M.D. , Aoki-Kinoshita K.F. , Kawashima S. , Yamamoto Y. , Yamaguchi A. , Okamoto S. , Kawano S. , Kim J.D. , Wang Y. , Wu H. , Kano Y. , Ono H. , Bono H. , Kocbek S. , Aerts J. , Akune Y. , Antezana E. , Arakawa K. , Aranda B. , Baran J. , Bolleman J. , Bonnal R.J.P. , Buttigieg P.L. , Campbell M.P. , Chen Y.A. , Chiba H. , Cock P.J.A. , Cohen K.B. , Constantin A. , Duck G. , Dumontier M. , Fujisawa T. , Fujiwara T. , Goto N. , Hoehndorf R. , Igarashi Y. , Itaya H. , Ito M. , Iwasaki W. , Kalaš M. , Katoda T. , Kim T. , Kokubu A. , Komiyama Y. , Kotera M. , Laibe C. , Lapp H. , Lütteke T. , Marshall M.S. , Mori T. , Mori H. , Morita M. , Murakami K. , Nakao M. , Narimatsu H. , Nishide H. , Nishimura Y. , Nystrom-Persson J. , Ogishima S. , Okamura Y. , Okuda S. , Oshita K. , Packer N.H. , Prins P. , Ranzinger R. , Rocca-Serra P. , Sansone S. , Sawaki H. , Shin S.H. , Splendiani A. , Strozzi F. , Tadaka S. , Toukach P. , Uchiyama I. , Umezaki M. , Vos R. , Whetzel P.L. , Yamada I. , Yamasaki C. , Yamashita R. , York W.S. , Zmasek C.M. , Kawamoto S. , Takagi T.
BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains
Journal of Biomedical Semantics. 2014. V.5. N1. 5 . DOI: 10.1186/2041-1480-5-5 WOS Scopus OpenAlex
Identifiers:
≡ Web of science: WOS:000343707900001
≡ Scopus: 2-s2.0-84988878542
≡ OpenAlex: W2157414955
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